TSOPPI resources

[danielvo]

Resources currently included in the TSOPPI, ICNVA and SADET images. Formatted as follows:
resource_name: [origin] usage

Dictionary:

• "NRC plots": Normalized Read Count (coverage) plots.
• "CNV" - Copy Number Variant
• "PON" - Panel Of Normals

TSOPPI images:

• resources
  • blacklisted_variants.tsv: [custom variant selection] currently not used, intended as a basis for exclusion from the small variant table
  • centromere_data (a directory with multiple files): [based on UCSC Genome Browser data] copy number plotting
  • TSO_500_LocalApp_v2.0.1.4_reference_files/CnvGeneThresholds.csv: [Local App resources] CNV plotting:
  • create_merged_normal_sample_CNV_data.tsv, merged_normal_sample_CNV_data.tsv: [custom, TSO500 normal samples] CNV distribution plotting (fold changes observed in normal samples)
  • TSO_500_LocalApp_v2.0.1.4_reference_files/TST500C_manifest.bed: [Local App resources] used as the source for the exon targets mentioned below
  • exon_targets (a directory with multiple files): [derived from Local App resources] coverage calculations
  • TSO_500_LocalApp_v2.0.1.4_reference_files/genome.dict: [Local App resources] not used
  • TSO_500_LocalApp_v2.0.1.4_reference_files/pepe_blacklist.bed: [Local App resources] referred to (in the 'BL' variant class definition) but not used
  • F1LCDx_genes.tsv: [compiled from F1L documentation] small variant table creation (information about Foundation One Liquid target genes)
  • PAR_genes.tsv: [compiled from the publication referenced in the header] used in absolute copy number calculations and for determining a valid set of controls (list of chromosome X genes that have two copies)
  • predisposition_genes.tsv: [compiled from the publication referenced in the header] predisposition variant table creation
  • rna_targets (a directory with multiple files): [Local App resources] RNA coverage plotting (not enabled in TSOPPI)
  • transcript_data (a directory with multiple files): [NCBI] RNA coverage plotting (not enabled in TSOPPI)
  • whitelist_data (a directory with multiple files): [custom resource] small variant whitelist (which genomic changes lead to the protein changes of interest?)
  • jdk-11.0.6, pcgr_databundle, picard_2.26.2.jar: [third party software/data]

ICNVA images:

• resources/data
  • 102_PON_centroid_unique.bed: [custom data derived from TSO500 normal samples] variant locations approved for PureCN analysis
  • 102_PON.filtered.bed: [custom data derived from TSO500 normal samples] CNV PON data
  • master_NRC_file.tsv: [custom data derived from TSO500 normal samples] observed normal sample target-wise coverages
  • normalDB_TSO500_hg19.rds: [custom data derived from TSO500 normal samples] CNV PON data
  • recognized_PureCN_options.tsv: [custom file] list of recognized PureCN options
  • custom_PureCN_options.tsv: [custom file] parameter setup for custom PureCN analysis
  • default_PureCN_options.tsv: [custom file] parameter setup for default PureCN analysis
  • default_NRC_gene_list.tsv: [custom file] the default list of genes for which NRC plots should be generated
  • valid_NRC_gene_targets.tsv: [custom file] a list of valid targets for NRC plots
  • vcf_header_template.txt: [custom file] a VCF header template
  • baits_hg19_intervals.txt: [PureCN reference data, compiled for the TSO500 assay] assay-specific data for PureCN analysis
  • hg19.simpleRepeat.bed: [PureCN reference data, compiled for the TSO500 assay] assay-specific data for PureCN analysis
  • mapping_bias_TSO500_hg19.rds: [PureCN reference data, compiled for the TSO500 assay] assay-specific data for PureCN analysis
  • PAR_genes.tsv: [compiled from the publication referenced in the header] used to determine a valid set of controls (list of chromosome X genes that have two copies)
  • TST500C_manifest.bed: [Local App resources] determining assay targets for NRC plotting
• resources/software
  • cowplot_1.1.1.tar.gz, picard_2.26.2.jar: [third party software]
  • create_VCF_body.py, format_NRC_data.py, output_PureCN_solution_details.R, plot_NRCs.R, TSOPPI_module.py: [custom scripts]

SADET images:

• resources/data
  • extraction_path_patterns.tsv
• resources/software: [custom file based on Local App output structure] file path patterns
  • check_LocalApp_error_logs.sh, TSOPPI_shared_functions.py: [custom scripts]

[marrip]

We should discuss if we can add the relevant files to the reference repo and, thereby, document how they were retrieved and make them readily available.